[gmx-users] Continuation 1) after crash and 2) in general

[David van der Spoel]

On Tue, 11 Dec 2001, Marc Baaden wrote:

>in a recent message spoel at xray.bmc.uu.se said:
>>> Kill the simulation and restart it from where the error in the xtc
>>> started (tpbconv -s topol -f traj -o cont -time 10000000) Fill in the
>>> right number for the time there. 
>
>I tried the tbpconv on a crash that happened recently. My only concern
>is, does it properly take into account shuffling ? Eg if the initial
>simulation was shuffled, will the continuation run be shuffled in the
>same way ?
I'm *quite* sure. The trr is shuffled and the tpr as well, since shuffling
occurs in grompp. Try it with a small membrane simulation, it will
certainly break if it's wrong...

>And a more general question: if I want to split my simulation of let's
>say 5 ns into chunks of 1 ns, what do I need in order to obtain the
>same thing as in one long simulation, eg no "discontinuities" at the
>simulation ends (1 ns intervals).
Basically not more than tpbconv, but there is one but. If you use
T-coupling the trajectories are not identical to what a single one would
be. There is nothing we can do about it right now, but it is on the
list...

>I mean, is it sufficient to write out coords+velocities at the end ?
>(Because due to the integration algorithm they should be t/2 shifted
>during a run, but what happens when you write them out ?)
V is written at half time steps.

>Is there a kind of model "restart-mdp" file ?
tpbconv -s topol.tpr -f traj.trr -o conv -extend 1000

>And is it always necessary to build a complete topology when you
>restart ? With eg AMBER you can use the same topology and just indicate
>the new coords/vels to start from and which time it is.
Right now tpbconv is as easy as it gets...

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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